8CE9 | pdb_00008ce9

Crystal structure of human Cd11b I domain in C121 space group

PDB DOI: https://doi.org/10.2210/pdb8CE9/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-01 Released: 2023-03-22
Deposition Author(s): Koekemoer, L., Williams, E., Ni, X., Gao, Q., Coker, J., MacLean, E.M., Wright, N.D., Marsden, B., Von Delft, F., Schwenzer, A., Midwood, K.
Funding Organization(s): University of Oxford, Medical Sciences Internal Fund (MSIF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.239 (Depositor), 0.216 (DCC)
R-Value Work:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human Cd11b I domain in C121 space group

Koekemoer, L., Williams, E., Ni, X., Gao, Q., Coker, J., MacLean, E.M., Wright, N.D., Marsden, B., Von Delft, F., Schwenzer, A., Midwood, K.

To be published.

Macromolecule Content

Total Structure Weight: 51.02 kDa
Atom Count: 3,207
Modeled Residue Count: 380
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-M	A [auth B], B [auth A]	215	Homo sapiens	Mutation(s): 0 Gene Names: ITGAM, CD11B, CR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens) Explore P11215 Go to UniProtKB: P11215
PHAROS: P11215 GTEx: ENSG00000169896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11215
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain P [auth A] SDF format, chain I [auth B] SDF format, chain C [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain P [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain P [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth B]	C [auth B], I [auth B], P [auth A], S [auth A], T [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain I [auth B] Focus chain P [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain C [auth B] Focus chain I [auth B] Focus chain P [auth A] Focus chain S [auth A] Focus chain T [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain AA [auth A]	AA [auth A] D [auth B] E [auth B] F [auth B] G [auth B] AA [auth A], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth A], Q [auth A], R [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.239 (Depositor), 0.216 (DCC)
R-Value Work: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.495	α = 90
b = 51.494	β = 132.961
c = 90.172	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
University of Oxford, Medical Sciences Internal Fund (MSIF)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.